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planemo upload commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
author tduigou
date Fri, 18 Nov 2022 16:36:16 +0000
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1 <tool id="rpscore" name="Score Pathway" version="@TOOL_VERSION@" profile="19.09"> 1 <tool id="rpscore" name="Score Pathway" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
2 <description>Computes a global score for a heterologous pathway.</description> 2 <description>Computes a global score for a heterologous pathway</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">5.12.1</token> 4 <token name="@VERSION_SUFFIX@">0</token>
5 <token name="@TOOL_VERSION@">6.0.1</token>
5 </macros> 6 </macros>
6 <requirements> 7 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">rptools</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">rptools</requirement>
8 </requirements> 9 </requirements>
9 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
10 python -m rptools.rpscore '$pathway' '$scored_pathway' 11 python -m rptools.rpscore '$pathway' '$scored_pathway'
11 --no_of_rxns_thres '$adv.no_of_rxns_thres' 12 --no_of_rxns_thres '$adv.no_of_rxns_thres'
12 --log "error" 13 --log "error"
13 ]]></command> 14 ]]></command>
14 <inputs> 15 <inputs>
15 <param name="pathway" type="data" format="xml" label="Pathway (rpSBML)" /> 16 <param name="pathway" type="data" format="sbml" label="Pathway (rpSBML)" />
16 <section name="adv" title="Advanced Options" expanded="false"> 17 <section name="adv" title="Advanced Options" expanded="false">
17 <param name="no_of_rxns_thres" type="integer" value="10" label="number of reactions above which a pathway is not scored" /> 18 <param argument="no_of_rxns_thres" type="integer" value="10" label="number of reactions above which a pathway is not scored" />
18 </section> 19 </section>
19 </inputs> 20 </inputs>
20 <outputs> 21 <outputs>
21 <data name="scored_pathway" format="xml" label="${tool.name} - ${pathway.name}" /> 22 <data name="scored_pathway" format="sbml" label="${tool.name} - ${pathway.name}" />
22 </outputs> 23 </outputs>
23 <tests> 24 <tests>
24 <test> 25 <test>
25 <!-- test 1: check if identical outputs are produced with default parameters --> 26 <!-- check if identical outputs are produced with default parameters -->
26 <param name="pathway" value="pathway.xml" /> 27 <param name="pathway" value="pathway.xml" />
27 <output name="scored_pathway" file="scored_pathway.xml" ftype="xml" compare="diff" sort="true"/> 28 <output name="scored_pathway" file="scored_pathway.xml" ftype="sbml" compare="diff" sort="true"/>
28 </test> 29 </test>
29 </tests> 30 </tests>
30 <help><![CDATA[ 31 <help><![CDATA[
31 rpscore 32 Score Pathway
32 ========= 33 ==============
33
34 34
35 Computes a global score for a heterologous pathway. The score is calculated from a learning process based on reaction rules score, flux balance analysis and thermodynamics metrics, and the number of reactions in the pathway. 35 Computes a global score for a heterologous pathway. The score is calculated from a learning process based on reaction rules score, flux balance analysis and thermodynamics metrics, and the number of reactions in the pathway.
36
37 36
38 Input 37 Input
39 ----- 38 -----
40 39
41 Required: 40 Required:
42 41
43 * **infile**\ : (string) Pathway file (rpSBML) with scores (rules, FBA, Thermo...) 42 * **Pathway (rpSBML)**\ : pathway file (rpSBML) with scores (rules, FBA, Thermo...).
44 * **outfile**\ : (string) Path to write pathway file (rpSBML) with global score 43 * **Scored pathway**\ : pathway file (rpSBML) with global score.
45 44
46 Advanced options: 45 Advanced options:
47 46
48 * **--no_of_rxns_thres**\ :(integer, default: 10) Number of reactions above which pathway are not scored (too long) 47 * **--no_of_rxns_thres**\ :(integer, default: 10) Number of reactions above which pathway are not scored
49
50 Version
51 ----------
52
53 5.12.1
54
55 Authors
56 -------
57
58 * **Jean-Loup Faulon**
59 * **Joan Hérisson**
60 48
61 Acknowledgments 49 Acknowledgments
62 --------------- 50 ---------------
63 51
64 * Thomas Duigou 52 * Thomas Duigou
53
65 ]]></help> 54 ]]></help>
55 <creator>
56 <person givenName="Jean-Loup" familyName="Faulon" email="jean-loup.faulon@inrae.fr" identifier="http://orcid.org/0000-0003-4274-2953" />
57 <person givenName="Joan" familyName="Hérisson" email="Joan.Herisson@univ-evry.fr" identifier="http://orcid.org/0000-0001-9741-0847" />
58 </creator>
66 </tool> 59 </tool>